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(-) Description

Title :  AZA-ACYCLIC NUCLEOSIDE PHOSPHONATES CONTAINING A SECOND PHOSPHONATE GROUP AS INHIBITORS OF THE HUMAN, PLASMODIUM FALCIPARUM AND VIVAX 6-OXOPURINE PHOSPHORIBOSYLTRANSFERASES AND THEIR PRO-DRUGS AS ANTIMALARIAL AGENTS
 
Authors :  D. T. Keough, D. Hockova, Z. Janeba, T. -H. Wang, L. Naesens, M. D. Edstei M. Chavchich, L. W. Guddat
Date :  10 Sep 14  (Deposition) - 07 Jan 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.53
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hypoxanthine-Guanine Phosphoribosyltransferase, Acyclic Nucleoside Monophosphonates, Malaria, 6-Oxopurine Phosphoribosyltransferase, 9- [(N-Phosphonoethyl-N-Phosphonomethoxyethyl)-2- Aminoethyl]Hypoxanthine, Cytoplasmic, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. T. Keough, D. Hockova, Z. Janeba, T. H. Wang, L. Naesens, M. D. Edstein, M. Chavchich, L. W. Guddat
Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors Of The Human, Plasmodium Falciparum And Vivax 6-Oxopurine Phosphoribosyltransferases And Their Prodrugs As Antimalarial Agents.
J. Med. Chem. V. 58 827 2015
PubMed-ID: 25494538  |  Reference-DOI: 10.1021/JM501416T

(-) Compounds

Molecule 1 - HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.4.2.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HPRT1, HPRT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HGPRT, HGPRTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
13L84Ligand/Ion[(2-{[2-(6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)ETHYL](2-PHOSPHONOETHYL)AMINO}ETHOXY)METHYL]PHOSPHONIC ACID
2MG8Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:68 , GLY A:69 , ARG A:100 , ILE A:136 , ASP A:137 , THR A:138 , GLY A:139 , LYS A:140 , THR A:141 , LYS A:165 , LYS A:185 , PHE A:186 , VAL A:187 , ASP A:193 , ARG A:199 , MG A:302 , MG A:303 , HOH A:410 , HOH A:414 , HOH A:428 , HOH A:430BINDING SITE FOR RESIDUE 3L8 A 301
02AC2SOFTWAREASP A:193 , 3L8 A:301 , HOH A:410 , HOH A:430BINDING SITE FOR RESIDUE MG A 302
03AC3SOFTWAREGLU A:133 , ASP A:134 , 3L8 A:301 , HOH A:427 , HOH A:428BINDING SITE FOR RESIDUE MG A 303
04AC4SOFTWARELYS B:68 , GLY B:69 , ARG B:100 , ASP B:134 , ILE B:136 , ASP B:137 , THR B:138 , GLY B:139 , LYS B:140 , THR B:141 , LYS B:165 , LYS B:185 , PHE B:186 , VAL B:187 , ASP B:193 , ARG B:199 , MG B:302 , MG B:303 , HOH B:407 , HOH B:412 , HOH B:425 , HOH B:430 , HOH B:432 , HOH B:433BINDING SITE FOR RESIDUE 3L8 B 301
05AC5SOFTWAREASP B:193 , 3L8 B:301 , HOH B:407 , HOH B:422 , HOH B:433BINDING SITE FOR RESIDUE MG B 302
06AC6SOFTWAREGLU B:133 , ASP B:134 , 3L8 B:301 , HOH B:425 , HOH B:430 , HOH B:431BINDING SITE FOR RESIDUE MG B 303
07AC7SOFTWARELYS C:68 , GLY C:69 , ASP C:134 , ASP C:137 , THR C:138 , GLY C:139 , THR C:141 , LYS C:165 , LYS C:185 , PHE C:186 , VAL C:187 , ASP C:193 , ARG C:199 , MG C:302 , HOH C:403 , HOH C:413 , HOH C:430BINDING SITE FOR RESIDUE 3L8 C 301
08AC8SOFTWAREASP C:193 , 3L8 C:301 , HOH C:430 , HOH C:431 , HOH C:432BINDING SITE FOR RESIDUE MG C 302
09AC9SOFTWAREGLU C:133 , ASP C:134 , HOH C:413BINDING SITE FOR RESIDUE MG C 303
10BC1SOFTWARELEU D:67 , LYS D:68 , GLY D:69 , ASP D:134 , ASP D:137 , THR D:138 , GLY D:139 , LYS D:140 , THR D:141 , LYS D:165 , LYS D:185 , PHE D:186 , VAL D:187 , ASP D:193 , ARG D:199 , MG D:302 , MG D:303 , HOH D:420 , HOH D:425BINDING SITE FOR RESIDUE 3L8 D 301
11BC2SOFTWAREGLU D:133 , ASP D:134 , 3L8 D:301 , HOH D:425BINDING SITE FOR RESIDUE MG D 302
12BC3SOFTWAREASP D:193 , 3L8 D:301 , HOH D:402BINDING SITE FOR RESIDUE MG D 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RAQ)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Leu A:67 -Lys A:68
2Gly B:57 -Gly B:58
3Leu B:67 -Lys B:68
4Leu C:67 -Lys C:68
5Ile C:116 -Gly C:117
6Gly C:118 -Asp C:119
7Asp C:119 -Asp C:120
8Leu D:67 -Lys D:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RAQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RAQ)

(-) Exons   (0, 0)

(no "Exon" information available for 4RAQ)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhh.......eeeeeee....hhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeee....ee...............eeeehhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4raq A   4 SPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKSDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    13        23        33        43        53        63        73        83        93       103|      129       139       149       159       169       179       189       199       209        
                                                                                                                             103|                                                                                                 
                                                                                                                              120                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhh.......eeeeeeee...eehhhhh..eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4raq B   4 SPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKIKVILSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    13        23        33        43        53        63        73        83        93       113  ||   127       137       147       157       167       177       187       197       207       217
                                                                                                                            102|  ||                                                                                                
                                                                                                                             113  ||                                                                                                
                                                                                                                                116|                                                                                                
                                                                                                                                 121                                                                                                


Chain C from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee........hhhhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh.....eeeeeee......hhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee..........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4raq C   5 PGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    14        24        34        44        54        64        74        84        94      |118       128       138       148       158       168||     179       189       199       209        
                                                                                                                          101|                                                  169|                                              
                                                                                                                           116                                                   171                                              


Chain D from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.......ee.hhh..hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhh.......eeeeeee.....hhhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4raq D   3 RSPGVVISDDEPGYDLDLFCIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKVIGDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISETGKAKYKA 217
                                    12        22        32        42        52        62        72        82        92       114  ||   126       136       146       156       166       176       186       196       206       216 
                                                                                                                            101|  ||                                                                                                 
                                                                                                                             114  ||                                                                                                 
                                                                                                                                117|                                                                                                 
                                                                                                                                 120
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4RAQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RAQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RAQ)

(-) Gene Ontology  (38, 38)

Asymmetric/Biological Unit(hide GO term definitions)

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    Leu A:67 - Lys A:68   [ RasMol ]  
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  4raq
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  HPRT_HUMAN | P00492
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HPRT_HUMAN | P00492: 1bzy 1d6n 1hmp 1z7g 2vfa 3gep 3ggc 3ggj 4ijq 4kn6 4rab 4rac 4rad 4ran 4rao 5brn 5bsk 5hia

(-) Related Entries Specified in the PDB File

4rab 4rac 4rad 4ran 4rao